The Aftermath
by daughterofathena2
Summary: The wedge between them is so deep that it takes millions of lives being in eminent danger for them to come together again. Centered around Ryan and Alex during the season finale and how they deal with the aftermath. Will include other characters. Please read and review.
1. Chapter 1

It was Liam? Ryan couldn't believe it, the man he had worked with for so long was a traitor, a terrorist. As he was sitting on the floor in the dorm room, tied up next to Miranda, Ryan relived the last few weeks in his head. Liam had asked him to tail Alex before Ryan even met her, and then Alex was framed for the bomb in New York. God Alex, how could he not have believed her? This whole time she was telling the truth and he just thought the worst of her.

"None of us knew, don't beat yourself up about it." Mumbled Miranda.

"Miranda?! Thank god you're alive, don't talk you need your oxygen." Said Ryan, but Miranda was already passed out again.

Ryan heard the sounds of banging doors below him, and he listened for the steps that would hopefully come closer.

"IN HERE! WE'RE IN HERE!" He screamed through his gag, trying his best to make himself heard, praying that whoever was in the building would find him and Miranda before Liam.

"HELP WE'RE IN HERE! WE'RE IN HERE! WE'RE IN HERE!" Ryan screamed again.

"Alex!" he heard Raina say, or was it Nimah? At that point he didn't care.

Alex and Raina rushed through the door, stowing their guns as they ran to check on Ryan and Miranda.

"She has a pulse!" said Raina.

Ryan breathed out in relief when Alex took the gag out of his mouth.

"Where is he?" she asked as she started working on the bonds on his wrists and legs.

"I don't know he left two or three minutes ago. Alex…Alex he has the bomb." Answered Ryan, taking the gag off his head. Ryan stood up with Alex and accepted the gun Raina offered him.

"She needs help. Find him." Said Raina, Ryan nodded and followed Alex out the door. Alex turned right and pushed Ryan away when he started to follow.

"We split up ok?" said Alex. Ryan exhaled and shook his head slightly, looking at Alex with desperate eyes he said

"If you do anything stupid…"

"Let's save the world and you can lecture me later."

"Alex!"

Alex didn't say anything else, just kissed him swiftly and took off down the hallway.

Ryan listened to Liam's deranged voice over the intercom as Alex tried to talk him down. As he entered another room, Ryan failed to check it completely when Liam rushed him and stuck a gun into his neck. Liam took Ryan's gun away and forced Ryan into the hallway, where Alex was waiting.

"Take the shot Alex I'll be fine." Urged Ryan, but Alex didn't listen. Liam continued to talk to Alex, about her father, about how the FBI was corrupted, how he had no choice about the things he had done. Alex let him talk, planning her moment just right. Without any change in her facial expression, she shot Liam in the head.

"The bomb's not here." Said Alex.

"Well then where is it?"

…

After Simon sacrificed himself to save everyone, Ryan pulled Alex into a hug.

"I'm so sorry, for everything." He mumbled into her hair. Alex just sobbed into his shoulder.

Caleb and Shelby were the first to leave, after a while Nimah coaxed Raina away from the scene, an ambulance arrived to take Miranda to the hospital.

"Do either of you need medical attention?" asked one of the paramedics.

"Are you hurt?" Ryan asked Alex, moving away slightly and cupping her face in his hands.

"No, I'm not. Are you?" Answered Alex.

"We're good, thanks." Ryan said to the paramedic, who nodded and moved away.

"Do you want me to drive you home?" Ryan asked Alex.

"I don't want to go home." Said Alex.

"Where do you want to go, or do you want to stay here for a bit more?" asked Ryan softly.

"Can we go to your place?" asked Alex.

"Yeah, of course. I need to figure what Liam did to my car but…" said Ryan.

"It's in the parking lot, I saw it when Raina and I got here." Said Alex.

"Good, are you ready to go?" asked Ryan, Alex nodded.

…

Later, at Ryan's apartment, Alex was sat on the couch with a mug of tea in her hands. Ryan knelt in front of her and took her face in his hands again. Alex looked into his pleading eyes.

" _Whenever_ you are ready, we need to talk about what happened over the past few weeks." Said Ryan, he wanted so much to tell her that he still loved her, that he never stopped but he didn't want to shock her even more tonight. Ryan stood up and was about to leave her alone when he hear her voice for the first time in hours.

"I'm ready to talk." Said Alex softly, setting her still steaming tea on the table.

Ryan sat down next to her and took her hands in his.

"Are you sure?" asked Ryan.

"The first time the terrorist…the first time _Liam_ called me was after the hearing. I said I believed Elias was acting alone because I was so tired of fighting, but I knew in my gut that something was wrong, and then I got the call. He sent me to a location, told me to tell no one. He sent me the video of Duncan killing himself. And then Natalie showed up, she also got a call which said to do what was asked or the people we cared about would get hurt. Liam wanted us to get information from the FBI's servers using your keycard and Hannah's fingerprint. We called in a bomb threat to get everyone out of the building. We got the information he wanted and sent it to him with a worm inside it, with the worm we tracked his location. But it was a trap, Natalie got killed by the explosion. That is why I showed up at your door hysterical that night." Started Alex.

"You said you wanted to be checked in somewhere, but in the next minute you were running out the door…Why? What happened?" asked Ryan.

"While you were on the phone, calling it in, I got messages from an unknown number. They were pictures of you and me at that very moment, to show that he was watching you." Said Alex.

"You ran out to protect me."

"I went to Simon next, I tracked him to a remote place in Vermont and he came back to help me. The next time I got a call, Simon put something in my phone that recorded the voice. Liam sent me a package of a pill bottle that was exactly like medication the Senator takes. He wanted me to swap out the pill bottles. I had the pills tested while Simon started trying to decode the voice. The pills were harmless, the only side effect was a raised body temperature. Hannah caught me trying to switch out the pills, so I told her the full story. She didn't believe me at first, she took the pills from me and kicked me out. But then I got another call saying that the pills had been switched, Hannah had done it for me. That night At Senator Haas' campaign event, when the blackout happened, we figured out that the Liam had technology that could see heat signature, and Senator Haas' body temperature was raised slightly above everybody else's. Before I realized what she was going to do, Hannah fired her weapon into the air and caused a panic, which was enough to save the Senator's life."

"Hannah got suspended for her actions, and I blamed you." Said Ryan.

"Finally, it was me and Simon who got to Will before you, we got him out of their but were forced to hand him over to the terrorist, who also took Simon and also had Shelby under his control. Shelby and I worked together, and we traced the voice back to a church where we found Will, dying of radiation poisoning. We got Will to a hospital and he told us that he was forced to help make a nuclear bomb. We tried to find Simon by searching for John Doe's with radiation poisoning, but we found Drew instead. Drew told me you were the voice and sent me with a usb drive that he said would uncover evidence on your computer, you found me and well, you know what happened after that. I got another call, seemingly from Drew in the garage and he told me to get into your truck with the bomb and drive. Somehow, Simon found me and he convinced me that the bomb wasn't live, and he told me that Drew was dead. You already know the rest of my story from there. What happened to you?"

"For a little bit, we had believed that Miranda was the terrorist; it was Liam who planted that idea into our heads. I went to Miranda's apartment and found a hidden camera, which told me that she was being watched too. Then I realized that Liam was missing from the office, I went to try and find Miranda and that's when Liam kidnapped me. I woke up tied next to Miranda with Liam just standing over us, smiling. He explained how he did everything, how he framed you for the first bomb and then all the rest of it. Finally he told us that he was going to blow up the building with all the new agents and us inside it, then he left the room with the bomb. I was so devastated, because I thought that I was going to die without being able to tell you that I'm sorry. Alex, I am so sorry I doubted you." Said Ryan.

"We doubted each other. And I'm glad it's over, I'm just sorry…I'm sorry it took so many lives. Elias, Duncan, Natalie, Drew…and Simon, they're all gone. I still can't believe what he did, what he had the courage to do." Alex broke down sobbing, leaning into Ryan as he held her.

Alex fell asleep from exhaustion, still in Ryan's arms. As gently as he could, Ryan picked her up and carried her to his room. He laid her down on the bed and tucked her in before returning to the couch.

Ryan woke up when Alex screamed. Ryan bolted up, grabbed his gun and rushed into the room to find Alex thrashing around on the bed, still screaming.

"Alex! Alex!" Ryan put his gun away and rushed to her side. Ryan tried to hold her down to stop her thrashing so she wouldn't hurt herself.

"Alex you're dreaming, please wake up! Wake up!" shouted Ryan, finally Alex's eyes opened, she was breathing heavily.

"You had a bad dream but it's over, you're safe, you're ok." Said Ryan, gathering her into his arms while pressing kisses to her forehead and her hair.

"Thank you." Said Alex.

"Always." Answered Ryan.

 **I'll continue if there's interest.**


	2. Chapter 2

The Aftermath ch2

 **The response I got to this story was just amazing, thank you so much to everyone who favorited, followed, and reviewed! The reason this chapter took so long is because I was trying to figure out where I would take this story, and then I had to figure out how to get that going and now it's been almost four months and I'm sorry. I hope you like the chapter.**

 **Have a giant piece of fluff.**

Alex slowly started to calm down from her nightmare.

"Do you want to talk about it?" asked Ryan softly.

"Not right now, can you just stay with me?" asked Alex.

"Yeah of course, try and go back to sleep, you need your rest" said Ryan.

"No more than you do" argued Alex.

"So we'll both sleep, how's that?" asked Ryan, grinning.

"Deal" answered Alex softly, already drifting off to sleep, Ryan not far behind her.

The following morning, Alex woke first. She quietly slid out from underneath the covers and walked into Ryan's kitchen. After getting a pot of coffee going, Alex looked around his kitchen, looking for anything edible.

The fridge was the obvious choice, but all that was in there was milk and leftover Chinese takeout that had clearly been there a while based on the smell.

"Yeah with all that's going on I haven't really had time to go grocery shopping, sorry." said Ryan as he leaned against the entranceway to the kitchen.

"It's ok. I can't really judge I mean I haven't had a home-cooked meal since I was home with my mom before I got Quantico" said Alex.

"I can cook us breakfast, just give me an hour to get the ingredients" said Ryan, grabbing his coat and heading for the door.

"Uh…Ryan?" asked Alex.

"Yeah?"

"Two things: Number one, you know you don't have to cook for me, right? And two, you do realize that you're still wearing pajamas, don't you?" said Alex.

Ryan looked down at his clothes and nodded.

"In answer, I want to cook for you and thanks for the reminder" said Ryan, walking back towards his bedroom.

"But…" protested Alex, before she could finish Ryan walked in front of her and placed his hand gently over her mouth.

"No 'buts', Alex. You spent so long taking care of others and forgetting to take care of yourself. Let me return the favor, if only this just this once." Ryan said softly before removing his hand from her mouth and was about to continue his way to his room when she held onto his arm to stop him. Ryan looked at Alex, confusion etched all over his face until she stood on her tippy-toes, put a hand on his cheek and kissed. Ryan immediately wrapped one arm around her waist and used the other to brush her hair back behind her ear. This kiss was short and sweet, but held so much emotion and both were smiling when they broke apart.

"At least let me come with you to the store" said Alex.

"Ok" answered Ryan.

They were out the door twenty minutes later, Ryan clad in jeans and a t-shirt and Alex wearing Ryan's sweatpants and an old t-shirt of his. Ryan drove to the closest grocery store and he and Alex held hands as they walked along the aisles.

"So are you going to tell me what you're planning on cooking?" asked Alex.

"I was thinking pancakes, my Nana's recipe. That sound good to you?"

"Sounds great"

"Great so we need flour, sugar, baking powder, salt, eggs, butter, and vanilla." said Ryan.

"And syrup" said Alex.

"Right"

"Ok let's split up, I'll get the dry ingredients and you get the other ones. Meet at the first checkout line when we're done?" asked Alex.

"I thought the point of you coming with me was so that we could shop together?" asked Ryan.

"Yes but this way we will get done in half the time and I'm starving. You should be too neither of us ate last night." Said Alex.

"Fair point, let's do it your way" conceded Ryan.

Alex finished first, as all the stuff on her list was all in one aisle. She pulled out her phone to see if anything had happened to the world since she last checked.

"Anything interesting on there?"

Alex looked up to find a man she didn't know looking at her.

"Not really, everything seems to have quieted down." Answered Alex before going back to stare at her phone.

"Come on, something on there has to be interesting if it's drawing you away from me."

"Do you want something?" asked Alex.

"Is a stimulating conversation too much to ask?" asked the man.

"Sorry, but you're going to have to find that somewhere else, I'm not in the mood to humor you." said Alex.

"Are you sure?" asked the man.

"Yeah, she's sure" said Ryan, coming up behind the man. The man turned around and looked up, as Ryan was quite a few inches taller.

"Ah…bye" said the man.

"I was handing it" said Alex with a glare.

"Yeah, but that was fun" said Ryan, smirking back at her.

Back at Ryan's, Alex and Ryan set the groceries on the table.

"Ok, where are your bowls?" asked Alex.

"Nope, I'm cooking, you're relaxing" said Ryan, taking her hand and leading her to his couch.

"I want to help" protested Alex.

"No, thank you. Let me cook for you, please" asked Ryan.

"You know you're lucky you're really good at the puppy dog eyes" said Alex.

Ryan smiled and kissed her.

"Sit, watch TV, I'll bring the pancakes out when their done" he said before disappearing back into the kitchen.

As Ryan moved around in the kitchen, he heard the TV turn on, but he tuned it out as he made the batter and turned on the stove. In no time at all, he had a stack of pancakes he split into two plates. Ran grabbed silverware, the plates and the syrup and brought them to Alex.

"Mm the pancakes smell amazing" said Alex.

"Wait till you try them before you pass judgement, you might change your mind" said Ryan, smiling and handing Alex her plate and the syrup. Alex poured a generous amount of syrup onto her pancakes before handing the bottle to Ryan who set it down on the table.

"What, you're not using syrup?" asked Alex.

"Don't need i0,t" answered Ryan

"You're weird," returned Alex.

"I love you," said Ryan.

"I know," said Alex.

The two ate in comfortable silence for a while, the dopiest smile on their faces. When Alex was done with her plate, she set it on the table before using her finger to eat some of the leftover syrup, sucking it off with her finger. Ryan watched her and suddenly his expression changed.

"Oh sorry does that gross you out?" asked Alex, noticing the change but failing to notice the syrup left on the corner of her mouth.

"No, not at all it's just… I think I need to reevaluate my opinion on syrup" said Ryan, setting his own plate down next to Alex's and moving closer to her. He reached for her desperately and brought his mouth to hers, kissing her hungrily. When he ran out of breath he broke away and placed kisses along her jawline and down her neck

"Are you sure about this? I can stop" said Ryan, looking Alex in the eyes.

"I don't want you to stop" answered Alex.

Ryan smiled and kissed Alex again. They shifted until Alex was lying back on the couch with Ryan hovering above her.

"Hey Ryan?"

"Yeah?"

"I love you too." Said Alex, smiling up at him. Ran smiled and dipped his head down, capturing her mouth in his.

 **Again, sorry this took so long. We'll get back to the FBI portion of this story next time. Thanks for reading!**

 **Please favorite/follow/review!**


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